Contacts of the helix formed by residues 213 - 221 (chain B) in PDB entry 1SY7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 3.1 31.4 - - + +
206B PHE* 4.7 4.3 - - + -
207B GLN* 3.5 24.5 - - - +
210B HIS* 3.0 17.4 + - + +
211B THR 3.0 0.6 - - - -
212B GLU* 1.3 78.4 - - - +
214B THR* 1.3 63.9 + - - +
215B HIS 3.4 1.8 - - - -
216B MET* 3.1 5.0 + - - +
217B PHE* 3.0 25.2 + - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 5.1 0.5 + - - -
210B HIS 4.4 0.4 + - - -
211B THR* 2.8 27.0 + - - -
212B GLU 3.3 0.8 - - - -
213B ALA* 1.3 77.9 - - - +
215B HIS* 1.3 61.5 + - - +
217B PHE* 3.4 22.2 + - + -
218B THR* 2.9 26.5 + - - -
463B HIS 3.6 9.2 - - - +
464B PHE* 4.0 23.9 - - + -
467B ALA* 3.8 16.4 - - + -
505B ARG* 4.3 6.6 + - - -
509B ILE* 3.9 21.3 - - + -
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Residues in contact with HIS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.9 13.9 - - + +
170B PHE 5.9 0.2 - - - +
212B GLU 4.5 5.8 + - - +
214B THR* 1.3 76.0 - - - +
216B MET* 1.3 64.3 + - - +
218B THR* 3.2 16.6 + - - -
219B TRP* 2.9 36.5 + + - -
321B THR* 2.8 33.4 - - - +
323B ILE* 4.0 9.8 - - + +
463B HIS 4.5 5.9 + - - +
466B GLN* 3.2 52.9 + - + +
467B ALA* 3.8 16.0 - - - +
470B PHE* 4.1 6.7 - - + +
541B LEU* 6.3 0.2 - - + -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.5 34.3 - - + -
165B ASN* 5.6 0.2 - - - +
167B ILE* 3.8 24.7 - - + -
169B VAL* 3.1 38.1 - - + +
170B PHE* 3.6 27.9 + - + +
171B PHE* 3.4 39.9 - - + +
212B GLU 5.2 0.2 + - - -
213B ALA 3.1 10.3 + - - +
215B HIS* 1.3 79.3 - - - +
217B PHE* 1.3 57.4 + - - +
219B TRP* 2.9 6.7 + - - +
220B ALA* 2.9 24.6 + - + +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 4.3 3.8 - - + -
203B PHE* 5.0 1.6 - - + -
204B TRP* 4.1 14.4 - + + -
207B GLN* 3.4 42.8 - - + +
213B ALA 3.0 23.4 + - - -
214B THR* 3.4 35.2 - - + -
216B MET* 1.3 76.3 - - - +
218B THR* 1.3 64.3 + - - +
219B TRP 3.3 0.2 - - - -
220B ALA* 3.6 9.6 - - + +
221B MET* 3.2 28.9 + - - +
486B PHE* 3.8 31.0 - + - -
502B MET* 3.8 21.3 - - + -
505B ARG* 4.0 11.0 - - + -
506B LEU* 4.2 1.6 - - + -
509B ILE* 3.8 18.4 - - + -
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B THR 2.9 18.2 + - - -
215B HIS* 3.2 10.1 + - - -
216B MET 3.0 0.8 - - - -
217B PHE* 1.3 79.2 - - - +
219B TRP* 1.3 64.5 + - - +
221B MET* 3.3 8.8 + - - -
222B SER 3.4 7.6 + - - -
467B ALA* 3.9 19.8 - - - +
470B PHE* 3.4 27.0 - - + -
471B TYR* 4.5 5.4 - - + +
482B MET* 3.4 26.7 - - + +
486B PHE* 4.7 5.2 - - + -
509B ILE* 3.6 22.0 - - + +
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Residues in contact with TRP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 3.7 33.6 - - + +
168B PRO* 3.4 38.8 - - + -
169B VAL* 3.8 11.8 - - + +
215B HIS* 2.9 51.2 + + - -
216B MET 2.9 7.4 + - - +
218B THR* 1.3 79.1 - - - +
220B ALA* 1.3 57.2 + - - +
222B SER* 2.6 32.1 + - - +
224B ARG* 3.7 48.2 - - + +
225B ALA* 4.6 0.5 - - - +
236B PHE* 5.3 2.0 - + - -
323B ILE* 4.5 3.4 - - + -
470B PHE* 3.3 40.4 - + - -
540B ASN 5.7 0.2 - - - -
541B LEU* 4.0 22.9 - - + -
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 3.2 24.7 + - + +
145B ASP* 6.4 0.4 - - - -
146B VAL* 5.6 5.6 - - + +
167B ILE* 4.5 6.7 - - + +
171B PHE* 4.7 14.6 - - + -
203B PHE* 5.3 4.0 - - + -
216B MET* 2.9 13.7 + - + +
217B PHE* 3.6 15.5 - - + +
218B THR 3.2 0.4 - - - -
219B TRP* 1.3 78.3 - - - +
221B MET* 1.3 67.9 + - + +
225B ALA* 3.2 17.3 - - + +
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Residues in contact with MET 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 3.4 19.2 + - - +
198B SER* 4.3 5.8 - - - +
203B PHE* 5.0 1.8 - - + -
204B TRP* 3.6 25.6 - - + -
217B PHE 3.2 17.2 + - - +
218B THR 3.3 4.9 + - - +
219B TRP 3.2 0.4 - - - -
220B ALA* 1.3 105.9 - - + +
222B SER* 1.3 63.2 + - - +
223B ASP* 5.4 0.2 - - - +
481B HIS 4.0 1.4 - - - +
482B MET* 3.4 16.6 + - + +
485B ALA* 3.4 34.4 - - + +
486B PHE* 3.6 36.6 - - + -
489B GLU* 3.6 28.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il